710.LC GRADUATE MOLECULAR BIOLOGY

 

Posted Material will be at:

http://biology.hunter.cuny.edu/molecularbio/

FALL 2011

Monday and Wednesday 5:30 - 7:40 PM

Room: 603 HW

 

Professors: Thomas Schmidt-Glenewinkel (TSG) / Paul Feinstein (PF)

E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it. (841 HN)

E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it. (904 HN)

 

Grading Scheme as follows:

TSG- 50%

PF-Only 5 of 10 quizzes count towards your grade: 40% total. Extra Credit quiz 11.

All quizzes given at the beginning of class.

PF-Homework: 10%

 

Background Textbooks (do not purchase unless you feel it is necessary):

Molecular Biology/Academic Cell Update by David P. Clark

ISBN 978-0-12-378589-3 or any good Molecular Biology textbook

 

(I like this book as well)

Recombinant DNA: Genes and Genomes - A Short Course, Third Edition (Watson, Recombinant DNA) [Paperback]

James D. Watson

http://www.amazon.com/Recombinant-DNA-Genomes-Course-Watson/dp/0716728664/ref=dp_ob_image_bk, Richard M. Myers, Amy A. Caudy, Jan A. Witkowski   

Course Description: This is a graduate level course in Molecular Biology aimed for giving students the ability to design experiments at the bench.

Learning Objectives: Understand genetic manipulation of a cell and the consequences of that manipulation to the functionality of that cell.

Be able to design experiments using the molecular biology learned in class.

Critically read published papers.

 

Pre-Req: Advanced Biology coursework: i.e. Biology and Biochemistry Majors.

 

August 29th, 2011 ( TSG) Lecture 1:  

August 31st, 2011 ( TSG) Lecture 2:  

Sept 7th, 2011 ( TSG) Lecture 3:  

Sept 12th, 2011 ( TSG) Lecture 4: 

Sept 14th, 2011 ( TSG) Lecture 5: 

Sept 19th, 2011 ( TSG) Lecture 6: 

Sept 21st, 2011 ( TSG) Lecture 7: 

Sept 26th, 2011 ( TSG) Lecture 8: 

Oct 3rd, 2011 ( TSG) Lecture 9: 

Oct 5th, 2011 ( TSG) Lecture 10: 

Oct 12th, 2011 ( TSG) Lecture 11: 

Oct 17th, 2011 ( TSG) Lecture 12: 

Oct 19th, 2011 ( TSG) Lecture 13: 

Oct 24th, 2011 ( TSG) Lecture 14: 

Oct 26th, 2011 ( TSG) Midterm Lect15

 

Oct 31st, 2011 (PF) Lecture 16:

What is a Euk Gene?  

Nov 2nd, 2011 (PF) Lecture 17 and Quiz 1: 8% of grade or not graded

PCR, Gene Synthesis, Codon Optimization

Nov 7th, 2011 (PF) Lecture 18 and Quiz 2: 8% of grade or not graded

Bacterial gene expression

Nov 9th, 2011 (PF) Lecture 19 and Quiz 3: 8% of grade or not graded

Cloning Vectors, lambda gt10, lambda gt11, BACs, YACs

Nov 14th, 2011 (PF) Lecture 20 and Quiz 4: 8% of grade or not graded

UAS-GAL4

Nov 16th, 2011 (PF) Lecture 21 and Quiz 5: 8% of grade or not graded

TMACl

Nov 21st, 2011 (PF) Lecture 22 and Quiz 6: 8% of grade or not graded

Sequencing, Next Gen Sequencing, Transcriptome Mapping

 

Two hybrid/One hybrid Systems

tetO-rtta (dox) tetO-tta

Nov 23rd, 2011 (PF) Lecture 23 and Quiz 7: 8% of grade or not graded

GFP/other live-cell indicators. Directed Evolution

Nov 28th, 2011 (PF) Lecture 24 and Quiz 8: 8% of grade or not graded

IRES/T2A/Translational (ribosomal) frameshifting

Nov 30th, 2011 (PF) Lecture 25 and Quiz 9: 8% of grade or not graded

Cre/Flp/Flex/BAC-homologous recombination

Dec 5th, 2011 (PF) Lecture 26 and Quiz 10: 8% of grade

Ura3 (complete KO of yeast genome)/ Transgenic mice

Dec 7th, 2011 (PF) Lecture 27: and Quiz 11: Extra Credit Quiz

Gene-targeting in ES cells/Zn-finger nucleases

Dec 12th, 2011 (PF) Lecture 28: Building Genomes/ Recitation for Homework

"Hunter College regards acts of academic dishonesty (e.g., plagiarism, cheating on

examinations, obtaining unfair advantage, and falsification of records and official

documents) as serious offenses against the values of intellectual honesty. The College

is committed to enforcing the CUNY Policy on Academic Integrity and will pursue

cases of academic dishonesty according to the Hunter College Academic Integrity

Procedures." If I find you are dishonest in your lecture work you will be reported.

Add a comment

Cincinnati Christian University

Syllabus: Biology GSC 220

Spring Semester 2013

 

Credit.3 semester hours, undergraduate credit

 

Course dates.Spring Term (January 24 – May 16, 2013)

Thursday evenings, 6:30 pm – 9:10 pm, room 105 in Presidents Hall

 

Instructor.Jeffrey D. Vassallo, Ph.D.

 

Email.This email address is being protected from spambots. You need JavaScript enabled to view it. (preferred) orThis email address is being protected from spambots. You need JavaScript enabled to view it.

 

Phone.513-478-8342 (please do not call after 10:00 pm)

 

Required text.Biology (Sylvia S. Mader) 11th edition

McGraw-Hill, 2013, ISBN: 978-0-07-352-550-1

Do not purchase the Laboratory Manual

 

Prerequisite.There are no prerequisites required to take this course.

 

Class rationale.This course partially fulfills the natural science requirement for undergraduate degrees at CCU.

 

Attendance and participation.The student is strongly encouraged to attend all class sessions and take thorough notes. Furthermore, students are encouraged to complete all reading assignments according to schedule so they are prepared to participate in classroom discussions and assessments.Every student must abide by the college’s attendance policy. A description of the policy is included in the college’s student handbook.You are only allowed two absences for this course, and every missed class, regardless of the cause counts toward your limit. Absences should be used wisely, especially if students are involved in athletics or other extra-curricular activities.

 

Academic Integrity.  Every student should abide by the college’s academic integrity policy. A description of the policy is included in the college’s student handbook.

 

Academic Support.  Students who require academic accommodations due to any documented physical, psychological or learning disability should request assistance from the Academic Support Director within the first two weeks of class. The Academic Support Office is located in the Lower Level of the Worship and Ministry Building (room 153). You may also contact the office by phone (244-8420).

 

Grading.                     25%     Quizzes

25%     Midterm exam

                                    25%     Final exam (comprehensive)

                                    25%     Research paper (due May 2)

Disclaimer.Grades will be administered in accordance with the scale published in the CCU catalog. However, the professor may make adjustments to the aforementioned grading policies in order to more adequately reflect learning outcomes. Requests for extensions, absences, and late work will be considered on a case-by-case basis.

 

Class preparation.Specified text material covered during each lecture should be read prior to class.Weekly homework assignments which cover the assigned reading and lecture material should be completed after the lecture. Homework assignments will be collected the following week during class. Although homework will not be graded, it is in your best interest to complete all assignments and turn them in on time. The homework assignments are intended to help you learn the lecture material and prepare for quizzes. Furthermore, if you complete all homework assignments, and turn them in on time,your lowest quiz grade will be dropped. On most weeks, quizzes will be given at the beginning of each class, and will cover the previously assigned reading, lecture material, and homework. Similarly, exams will cover assigned reading, lecture material, and homework.In addition to class participation, weekly forums will be set up in Moodle to facilitate further discussion on important class topics. Although it is not expected for you to participate in all forum discussions, it is in your best interest to read them and contribute, as these topics will help you in writing your research paper. Furthermore, exam questions may come directly from forum discussions.

 

Instructor/student agreement.As your instructor, you can expect that I will always come to class prepared to teach.Furthermore, I will be available for questions as needed either by email, phone, and before and after class. If you contact me by email or phone you can expect a response within 24 hours. Additionally, I will have all graded assignments returned in a timely manner so you are aware of your performance.

 

As the student, I expect that you will always come to class prepared and eager to learn. Furthermore, I expect you to have respect for everyone else in the class, this includesno phone use, computer use or talking which distracts those around you. We are learning in a community. Therefore, we all have a responsibility to contribute to the success of this learning environment, which includes participating in class and forum discussions. If class topics become controversial it is important to be critical of ideas, and not the individual, as respect of others is absolutely critical for a successful learning environment.

 

Course description and goals.This is an introductory biology course for non-science majors. The primary objectives of this course are1) to introduce students to the process of scientific inquiry, critical thinking skills and communication, 2) to provide a knowledge base in the biological sciences that enables life-long learning, 3) to discuss contemporary issues in biology and their implications on society, and 4) to explore the interface between science and faith.

 

  1. Scientific inquiry, critical thinking skills, and communication
    1. Develop critical thinking skills for evaluating scientific claims
    2. Understand the limitations and biases of scientific inquiry
    3. Learn how to ask scientific questions and develop hypotheses
    4. Defend theories and models based on evidence
    5. Demonstrate the ability to read and understand scientific literature written for the educated layman
    6. Develop the ability to effectively write about and discuss controversial topics in biology

 

  1. Knowledge base in the biological sciences that enables life-long learning
    1. Unifying concepts of life
    2. The process of science
    3. The chemistry of life
    4. Cell structure and function
    5. Cellular processes essential for sustaining life
    6. Genetic basis of life
    7. Molecular biology of the gene
    8. Anatomy and physiology
    9. Microbiology
    10. Plants
    11. Evolution
    12. Behavior and ecology

 

  1. Contemporary issues in biology and their implications on society
    1. Discuss how progress in biology is determined in part by personal, political, social, economic, cultural and ethical influences
    2. Understand the impact of science and technology on society
    3. Identify ethical issues which have developed from new technology

 

  1. Interface of science and faith
    1. Identify limitations of scientific inquiry and faith
    2. Learn theories of biology which are consistent or in conflict with the Bible
    3. Learn methods for integrating science and faith

Course outline

 

Date

Lecture and other activities

Topic

January 24

1

Course expectations

Study of life, chemistry of life and the process of science

Overview of the research project

January 31

2

Quiz 1

Cell structure and function

Research project – sources of information and critical evaluation of evidence

February 7

3

Quiz 2

Cellular processes essential for life

February 14

4

Quiz 3

Research paper topic due

Genetic basis of life (cell cycle, mitosis and meiosis)

 

February 21

5

Quiz 4

Genetic basis of life (Mendelian genetics)

 

February 28

6

Quiz 5

Molecular biology of the gene

Overview of scientific and persuasive writing

March 7

Spring break – no class

March 14

7

Quiz 6

Outline of research paper due

Biotechnology

Contemporary issues in biology

Interface of science and faith

March 21

8

Midterm exam

Anatomy and physiology

 

March 28

9

Quiz 7

Anatomy and physiology

April 4

10

Quiz 8

Anatomy and physiology

April 11

11

Quiz 9

Draft of research paper due

Microbiology

April 18

Community service day – no class

April 25

12

Quiz 10

Plants

 

May 2

13

Quiz 11

Research paper due

Evolution

 

May 9

14

Quiz 12

Behavior and ecology

May 16

Final exam

 

Disclaimer.Your professor reserves the right to make changes to the contents of this course plan as we proceed through the semester. Extenuating circumstances might promptthe professor to make adjustments to the schedule, assignments or grading. Furthermore, all topics listed above may not be covered in class. However, students will be given advanced notice of any schedule changes.

 

Research project.  The goal of this research project is to develop a persuasive essay on acontroversial topic in biology. Specifically, the student should focus on critical thinking skills,communication, an understanding of the limitations and biases of science, and develop an ability to read and understand the scientific literature in a particular area of biology. An additional goal of this research project is for the student to explore the influence of science and faith in contributing to their position and conviction as well as the perspective of their audience.

 

“To simply be a creationist and argue that evolution is wrong because the Bible says creation is right makes one look foolish in the secular world. Learning how to interface science and faith, in a manner that allows you to recognize biases and limitations of both sides,lends credibility to your position, and makes your argument more compelling.”

 

  1. General guidelines.Discussing your research project with peers or anyone else that you find suitable is encouraged. However, students are expected to write their own research paper. The paper should be typed (Times New Roman, font size 12) with one inch margins and double spaced with a total length of 7-10 pages, excluding the title page, references, tables and figures. Note tables and figures can be used for illustrative purposes. Proper grammar, spelling and a logical progression of thought are important for this project as your credibility is increased when you are able to communicate effectively.

                                   

  1. Audience: Any person with an opposing worldview. However, please define this individual and provide context regarding religious, cultural, economic, political or other bias, which may influence their position.Possible suggestions include an atheist, agnostic, Hindu, Muslim, Catholic, Protestant, theistic evolutionist or simply a friend with a similar worldview but a different position on this particular topic.

 

  1. Title page. Include title, author name and date.

 

  1. Introduction (~2 pages). Define the controversial issue by providing sufficient background (e.g. biology, political, social, cultural and ethical factors) to entice the reader why they should read more. Inform the reader of your position, and that you intend to provide compelling evidence to support your position and persuade the reader that they should adopt your way of thinking.

 

  1. Body (4-6 pages).Provide sufficient background in biology for the reader to understand why the issue is controversial. Discuss current and historical trends and theories and how they have changed over time with the influence of different factors (e.g. political, social, cultural, and ethical).Provide relevant perspective on both sides of the issue and clarify important points. Build a logical argument by providing clear and compelling evidence from reliable sources to support your argument. Also, note limitations and potential biases of evidence and conclusions.

 

  1. Conclusion (1-2 pages).Do not simply restate the results. Instead, refer to the introduction and summarize the goal of this research project. Present a reflective succession of important arguments that logically lead to the development of your conclusion. The reader should be left thinking that your conclusion is based on agreed upon facts and shared values. Consider whether your conclusion is biased based on science, faith or both and how this adds or detracts credibility to your position.

 

  1. References (1 page). Provide a minimum of 5 references (CCU format), and cite them within the text. You can use whatever references you would like including peer reviewed scientific journals (e.g. Science and Nature), newspaper articles and Wikipedia. However, it is important to consider the reliability of the source. Just because something is printed in the most respected scientific journal does not make it true. Journal articles with profound scientific discoveries have a high retraction rate. Similarly, you should not automatically discount scientific information from what may appear to be an unreliable source, as personal, public, political, and cultural opinions of science are often influenced by these sources. Therefore, the reference you cite should be dictated in part by what you are trying to convey to your audience. Recognize that all sources of information have limitations and biases and that your perspective and their reliability may be different from that of your audience.Sources of information should be selected which help you 1) to critically evaluate the reliability of information,2) enable you to formulate your own educated opinion, and 3) facilitate effective communication ofyour argument.

 

Although there are a variety of tools available for conducting this type of research I would encourage you to useOhioLink (www.ohiolink.edu/) and Pubmed (http://www.ncbi.nlm.nih.gov/pubmed/). We will go over a demonstration of how to use these search engines in class.

 

Grading of research project.            25% Meet deadlines, formatting, grammar and spelling       

                                                            25% Define topic and provide relevant perspective

                                                            25% Define biases and limitations of evidence

                                                            25% Develop logical and compelling argument

                                                                                   

Proposed controversial topics.This is not intended to be an exhaustive list but rather proposed topics for you to consider. If you have a particular topic of interest please submit it to me for approval. Most of these issues will be discussed to some extent during class.

 

  1. Should embryonic or adult stem cellsbe used in research, organ regeneration, saving or extending human life? If no, how do you defend this position to terminally ill patients that could benefit from such therapy?
  2. Is the theory of evolution sufficient to explain the origin of life? If not, how do you defend alternative theories? Does it really matter what you believe regarding the origin of human life?
  3. Should genetically modified organisms be pursued as a way to address theworldwide food shortage? Consider the potential benefits and risks of this technology?
  4. Recent biological research suggests future human life expectancy may increase beyond100 years. Do you think this is possible? If yes, what are the advantages and disadvantages of this outcome?
  5. Should animal and human cloning be pursued? If yes, what are the benefits and risks of this technology?
  6. There is a common belief thatcosmetics derived from all natural products are safer and more effective than manmade products. Is there evidence to support this claim? Are all natural products really safer than manmade products?
  7. There is a common belief that the cure for cancer is already known but drug companies are holding back the cure to make money. Is this a reasonable hypothesis supported by scientific evidence or simply another conspiracy theory?
  8. There is an active effort to prevent the use of animals in research. Should animals be used for research? Consider the fact that pharmaceutical drugs require testing by the FDA on animals before humans for efficacy and safety reasons. If you are against the use of animals for research would you support the use of a drug tested on animals if it would save your terminally ill child?
  9. Are you against abortion? If so, why? Consider the biological and legal definition of life. How would you defend your position?
  10. Recent political changes have set the precedent for legalization of illegal drugs. What is a drug? Should all drugs be legal? What are the benefits and risks of legalizing all drugs?
  11. There is a conspiracy theory suggesting vaccines are the cause of autism. What is the basis for this causal relationship? Do you agree with this claim and is there sufficient evidence to support or refute the claim?
  12. Obesity and the metabolic syndrome have reached epidemic levels in this country. Do you think this major public health issue is caused by genetic, environmental, cultural or personal choices? Consider whether this is a public health issue in other countries.
  13. Diet and exercise programs continue to increase in popularity yet obesity continues to become a growing public health concern in this country. What is most important in maintaining a healthy living style, and why do these diet and exercise programs often fail?

 

Add a comment
update.pk ||You are 1127941 visitor